Contacts of the helix formed by residues 296 - 304 (chain A) in PDB entry 6VSB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 296 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ASP* 3.1 14.9 + - - +
295A PRO* 1.3 77.0 - - - +
297A SER* 1.3 62.1 + - - +
299A THR* 2.5 35.4 + - - +
300A LYS* 3.0 32.0 + - + +
308A VAL* 3.9 22.9 - - + -
599A THR* 4.2 10.8 - - + +
602A THR* 4.7 5.8 - - + +
605A SER 5.5 0.4 - - - +
606A ASN* 3.6 35.2 - - + +
608A VAL* 3.7 31.9 - - + +
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Residues in contact with SER 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A VAL* 4.7 7.3 - - - +
290A ASP 3.2 32.2 + - - -
293A LEU* 4.4 9.4 - - - +
294A ASP* 2.4 30.0 + - - -
296A LEU* 1.3 77.8 - - - +
298A GLU* 1.3 60.7 + - - +
299A THR 3.0 1.3 + - - -
300A LYS* 3.9 14.9 + - - +
301A CYS* 3.2 28.9 + - - -
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A CYS* 4.0 22.3 + - - +
292A ALA* 5.5 2.9 - - - -
294A ASP 3.1 11.7 + - - +
295A PRO* 3.6 19.3 - - - +
296A LEU 3.1 1.2 - - - -
297A SER* 1.3 75.6 - - - +
299A THR* 1.3 53.8 + - - +
301A CYS* 4.2 3.1 - - - +
302A THR* 3.4 11.8 + - - +
315A THR* 2.5 43.8 + - + +
316A SER* 2.9 29.7 + - - -
595A VAL* 4.9 2.9 - - - +
597A VAL* 5.9 0.7 - - - +
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PRO 3.5 9.2 - - - +
296A LEU* 2.5 35.5 + - - +
298A GLU* 1.3 77.6 - - - +
300A LYS* 1.3 64.2 + - - -
301A CYS 3.1 1.1 - - - -
302A THR* 3.3 7.4 - - + +
303A LEU* 2.9 28.9 + - - +
308A VAL* 4.3 9.2 - - - +
313A TYR* 4.9 13.0 - - + +
315A THR* 3.6 25.1 - - + -
597A VAL* 3.4 31.0 - - + +
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Residues in contact with LYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LEU* 4.6 1.2 - - - +
289A VAL* 3.7 32.4 - - + +
296A LEU* 3.0 33.6 + - + +
297A SER* 3.9 16.9 + - - +
299A THR* 1.3 75.6 + - - +
301A CYS* 1.3 56.6 + - - +
303A LEU 3.6 0.2 - - - -
304A LYS* 2.8 24.3 + - - -
305A SER 3.0 27.8 + - - +
306A PHE* 3.6 26.3 + - - +
308A VAL* 3.9 15.4 - - + +
602A THR* 3.9 18.1 - - - +
606A ASN* 4.9 3.4 - - - +
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Residues in contact with CYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LEU* 4.0 12.1 - - + +
289A VAL* 3.6 22.2 - - - -
291A CYS* 2.0 55.0 - - + -
297A SER 3.2 17.2 + - - +
298A GLU 4.3 4.0 - - - +
299A THR 3.1 0.6 - - - -
300A LYS* 1.3 77.1 - - - +
302A THR* 1.3 62.3 + - - +
304A LYS* 2.8 32.2 + - - +
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Residues in contact with THR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A GLU 3.4 4.8 + - - +
299A THR* 3.3 16.6 - - + +
301A CYS* 1.3 77.9 - - - +
303A LEU* 1.3 62.0 + - + +
304A LYS* 4.8 4.9 - - - +
313A TYR* 6.1 1.6 - - + -
314A GLN 4.3 7.4 + - - +
315A THR* 3.3 45.3 + - - +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A THR* 2.9 17.4 + - - +
300A LYS 4.1 1.6 - - - +
302A THR* 1.3 79.5 - - + +
304A LYS* 1.3 71.6 + - - +
305A SER* 4.3 10.5 - - - +
308A VAL* 3.8 34.5 - - + -
309A GLU* 4.4 7.9 - - - +
313A TYR* 4.2 26.7 - - + -
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Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.3 24.0 - - + +
50A SER* 3.2 31.1 + - - +
276A LEU* 3.8 15.2 - - + +
300A LYS 2.8 8.2 + - - -
301A CYS 2.8 20.1 + - - +
302A THR* 4.8 3.5 - - - +
303A LEU* 1.3 81.9 - - - +
305A SER* 1.3 57.8 + - - +
964A LYS* 5.6 13.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il